Notre Dame's president ripped the NCAA's decision to deny the school's appeal to restore 21 vacated football victories from an academic misconduct violation, saying the association "perverted" the notion that universities determine how they police academics.

The NCAA denied Notre Dame's appeal Tuesday, wiping off the books all 12 wins from the Fighting Irish's 2012 national championship game run under coach Brian Kelly.

In a letter to Notre Dame alumni , University President Fr. John Jenkins says the penalty was unprecedented considering who was involved in the misconduct, and the school was being punished for rigorously enforcing its honor code. He called the ruling unfair, referencing the recent North Carolina case in which the NCAA did not punish the school after an investigation of athletes taking irregular courses.

The appeals committee was not swayed and upheld the penalty passed down in November 2016 by the committee on infractions.

Notre Dame agreed to accept certain NCAA findings and acknowledged cheating involving several football players and a student athletic trainer, but appealed only the penalty that vacated victories.

The NCAA also fined the school $5,000 and placed it on one years' probation after finding academic misconduct orchestrated by the trainer.

The NCAA said the trainer was employed by the athletic department from the fall of 2009 through the spring of 2013 and "partially or wholly completed numerous academic assignments for football student-athletes in numerous courses" from 2011 into 2013.

It said she did substantial coursework for two players and gave impermissible help to six others in 18 courses over two academic years.

In all, the NCAA said, three athletes ended up playing while ineligible, one during the 2012 season, which ended with a lopsided loss to Alabama in the BCS championship game, and the other two the following season, when the Irish went 9-4.

In his letter, Jenkins said the players were retroactively declared ineligible after Notre Dame investigated the misconduct in 2014 and recalculated the students' grades.

Jenkins said had Notre Dame merely expelled the students instead of recalculating grades, had a statute of limitations for past offenses or chose not to punish the students, an NCAA penalty would not have been imposed.

"The NCAA has not chosen to ignore academic autonomy; it has instead perverted it by divorcing it from its logical and necessary connection to the underlying educational purpose," Jenkins wrote.

The vacation of victories was a discretionary penalty. Notre Dame objected to the penalty, noting all previous NCAA academic misconduct cases that resulted in victories being vacated involved an administrator, coach, or person who served in an academic role.

"This is more disturbing given that, in 2016, the member institutions of the NCAA amended the academic misconduct rules to make clear that students who serve in roles identical to the student in our case would not be considered institutional representatives," Jenkins wrote.

The appeals committee said in its report that the committee on infractions did not abuse its discretion when it determined the student trainer was an institutional employee.

"When reviewing infractions cases, the Committee on Infractions uses the bylaws and interpretations contemporaneous to the conduct being reviewed," the appeals committee wrote. "Therefore, under the bylaws in place at the time of the violations, a student trainer would be considered an institutional employee."

In its report, The appeals committee confirmed that at the time of the violations, the athletic training student was considered a university employee under NCAA rules.

Jenkins didn't name the North Carolina case but referred to a "recent high profile academic misconduct case in which the NCAA Committee on Infractions chair explained that even though certain classes `more likely than not' were used to keep athletes eligible with fraudulent credits, the legitimacy of those classes was beyond the jurisdiction of the NCAA's enforcement process precisely because that question must be left to the determination of the university in the exercise of its academic autonomy.

"The notion that a university's exercise of academic autonomy can under NCAA rules lead to exoneration - or to a severe penalty - without regard to the way it which it is used defies logic and any notion of fundamental fairness," Jenkins said.

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